Bacterial Community Structure in the Hindgut of Wild and Captive Dugongs (Dugong dugon)

Abstract

Dugongs (Dugong dugon) are marine mammals that obtain nutrients through hindgut fermentation of seagrass, however, the microbes responsible have not been identified. This study used denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing to profile hindgut bacterial communities in wild dugongs. Faecal samples obtained from 32 wild dugongs representing four size/maturity classes, and two captive dugongs fed on cos lettuce were screened using DGGE. Partial 16S rRNA gene profiles of hindgut bacteria from wild dugong calves and juveniles were grouped together and were different to those in subadults and adults. Marked differences between hindgut bacterial communities of wild and captive du gongs were also observed, except for a single captive whose profile resembled wild adults following an unsuccessful reintroduction to the wild. Pyrosequencing of hindgut communities in two wild dugongs confirmed the stability of bacterial populations, and Firmicutes (average 75.6% of Operational Taxonomic Units [OTUs]) and Bacteroidetes (19.9% of OTUs) dominated. Dominant genera were Roseburia, Clostridium, and Bacteroides. Hindgut microbial composition and diversity in wild dugongs is affected by ontogeny and probably diet. In captive dugongs, the absence of the dominant bacterial DNA bands identified in wild dugongs is probably dependent upon prevailing diet and other captive conditions such as the use of antibiotics. This study represents a first step in the characterisation of a novel microbial ecosystem-the marine hindgut of Sirenia.

Variation in the hindgut microbial communities of the Florida manatee,Trichechus manatus latirostrisover winter in Crystal River, Florida

“…. The closest sequence similarity matches using the blast algorithm against the NCBI GenBank and Greengene databases and wild dugong amplicon sequence data set (Eigeland et al ., ) are contained in the Supporting Information, Table S1. Core OTUs that could be classified to the level of genus included Adlercreutzia, Bacteriodes, Butyrivibrio , Caloramator, Cellulosilyticum, Clostridium , Eubacterium, Ruminococcus and Sedimentibacter .…”

“…Bacterial phyla found in the manatees of this study were similar to those that dominate the hindgut flora of the related wild dugong in eastern Australia (Eigeland et al ., ) with Firmicutes (76% of flora) and Bacteroidetes (20%) being dominant, and Actinobacteria and Proteobacteria being the next most prevalent phyla. Further, from six bacterial phyla identified in a single captive dugong held in Japan (Tsukinowa et al ., ), a similar distribution was observed: Firmicutes 83.1%, Bacteroidetes 15%, with the remaining phyla ( Verrucomicrobia , Actinobacteria , Lentisphaerae and Proteobacteria) at < 1%.…”

“…Two OTUs (OTU 5326, 2156) were congruous with uncultured Clostridium species clones found within the faecal microbiota of a captive dugong (Tsukinowa et al ., ). Furthermore, comparison of the manatee's 23 core OTUs with a barcoded 16S rRNA gene amplicon database from wild dugong faecal samples (Eigeland et al ., ) identified 11 OTUs, including six of the dominant OTUs, with high sequence homology to dugong OTUs (using the blast algorithm). Given the sympatric evolution of sea cow communities (Velez‐Juarbe et al ., ), this similarity in hindgut bacterial flora might be expected.…”

Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing

“…This cDNA was then used as template for the production of 16S rRNA gene amplicons for pyrosequencing (see Supplementary Material 8 for detailed PCR protocol). Sequence data were processed, clustered into operational taxonomic units at the 97% identity level and classified as described previously (Eigeland et al, 2012;Gulino et al, 2013). All data processing was performed in QIIME 1.5.0 (Caporaso et al, 2010).…”

Composition of gut microbiota in infants in China and global comparison

“…Liu D et al 14 used 16S rDNA PCR-DGGE methodology to provide a profile of the dominant gut microbiota of Chinese neonates, but the PCR-DGGE method used may limit the generalizability of their results. It has been previously demonstrated that species richness and diversity were higher for the samples analyzed by 454-pyrosequencing than DGGE15.…”